“If we can assemble genomes, we can learn some of these strategies to reduce bias.”
I study the role of secondary metabolites, especially defensive chemistry and how they influence plant-fungal interactions. For my Ph.D., I’m studying a mushroom called Amanita phalloides, the death cap mushroom. It’s native to Europe but it was brought overseas in soil of plants and trees. It’s now present on every other continent except for Antarctica. And it’s super poisonous. It’s the number one cause of death in humans from mushroom poisonings, and we don’t know what its toxins are doing in the field. We don’t know if this mushroom is poisoning other microbes in the soil, or if it’s having an effect on insects.
How have you collaborated with JGI?
For my master’s program, I studied these fungal seed pathogens of wild Bolivian chili peppers. It turns out that the chili peppers make the spice to fight off these fungi that get into the fruit and kill the seeds. And I was really interested in how the fungi that we’ve isolated out of the Bolivian fruits have evolved such a strong tolerance to the spice. These are these wild isolates. I know their genus from sequencing the ITS (internal transcribed spacer) region, but I can’t knock out genes of them because we don’t know what they are. And so one of the things that I’m doing with the JGI through the 1,000 Fungal Genomes Project will be sequencing one of those mystery isolates from the chili pepper collection. We think it’s a Phomopsis species based on the ITS. It’s really tolerant of spice, and we have evidence that it has a few that aren’t in the mitochondrial membrane itself, but floating around.
Based on the results I got from research I did during my masters program, we think this isolate has a bunch of different respiratory enzymes. It also seems to have an enzyme that can break down capsaicin, which could be really useful for a few different reasons. It could help people that don’t like spice and want to break it down in their food a little bit—a Beano of sorts for spice. And the enzyme could also be used to treat people that might get pepper sprayed, or get other types or sort of capsaicin in their eyes.
Why is this research important?
A lot of different people study fungal pathogens. And it turns out that a lot of fungi develop their virulence or their tolerance of other things in the plants through resistance genes – these sort of gene-for-gene interactions that happen between the plant and the fungus. What’s cool about my chili fungi that they’re tolerant of capsaicin for several different reasons. They’ve got these alternative respiratory enzymes, they seem to have the enzyme to break down capsaicin, and they might have transporters that can spit out the spice. It’s a really complicated resistance, and this happened over many years of evolution.
There’s not just one way that the fungi are resistant to capsaicin. I hope that this knowledge might be useful both for protecting plants from fungal pathogens, as well as just in terms of the general evolutionary theory—why these plants evolve, and how they do it. I think secondary metabolites can be a really strong driver of evolution and they might explain not just resistance genes, but a lot of other physiology that happens in the fungus.
What do you value about JGI’s contributions?
As a grad student, I think that JGI has a lot to offer. While working on the sequence of my Phomopsis genome, I get access to a bunch of these protocols to get really high quality, high molecular weight DNA and high quality RNA. So just having access to those protocols is really useful. I also think that since I am just learning about the bioinformatics involved in assembling a genome, it’s great that they have those online tools and people you can talk to who that are really helpful to teach you how to analyze your data, how to assemble your genome, and how to annotate it. And there are a lot of databases that will be really useful when we’re trying to figure out which are the enzymes that are involved in the spice tolerance. We can compare them to other known fungi to try figure out what those enzymes are.
Anything else you’d like to add?
One of the great things about being at UC Berkeley is that the Joint Genome Institute is nearby, so there are people who work that there that are experts in genomics that also teach classes at Berkeley. I took a fungal genomics class from Igor Grigoriev, and learned about some of the tools that were offered at JGI and resources that are also available online to answer the questions anyone excited about comparative genomics might want to answer.
The 2017 JGI User Meeting was lot of fun. I had a really good time. It was the first time I got to give a talk about unconscious bias to people that didn’t necessarily come to hear about bias. People were really appreciative that the JGI cares about diversity and about ways that we might not be as kind to each other as we intended. Everyone was happy to hear what I had to say, and excited to hear that there are reliable tools to fix this. It’s not an impossible problem. It’s manageable, and we’ve got the motivation to fix this. If we can assemble genomes, we can learn some of these strategies to reduce bias.